opal_instructions.txt

Instructions for setting up a new study in the Opal server

Opal javascript code

https://opaldoc.obiba.org/en/latest/magma-user-guide/value/value.html

1. Have a data dictionary ready

    see projects/meat_project/meat_data_dictionary2.xlsx

2. Find a way of splitting the data by country using R - can either use the CSV or Stata file. 
The advantage of the Stata file might be that it preserves some metadata for uploading into Opal.

Use R script meat_study.R

3. Upload the data dictionary, data (in Stata format) and create the table. Instructions are here:

https://gitlab.inesctec.pt/wp4-recap/wp4_workshop/-/wikis/opal

    a. Upload the data
    b. Upload the data dictionary as an xls file (this should have harmonization Java code)
    c. Click on import data to import data and create a table
    d. Click on create view to link this table to a view. This will also ask for data dictionary
        which has hamronization script. This will ultimately create a harmonized view.

4. Create a view by 

    a. selecting the table
    b. selecting the data dictionary xls file. The file is called meat-harm-dictionary.xlsx
       This will also have java script code for data harmonization.
          
   This will create a harmonized view.     

5.  If the categories in the harmonised data are lost then
    a. Go to each view, 
    b. make sure you are looking at Dictionary,
    c. Click + Add Variables,
    d. Choose Add/update variables from dictionary, 
    e. Choose the file meat_harm-dictionary2.xlsx

6. Connect to Opal server from R Studio and write analyst code. See survival_testing_code.R